Fig. 2: Human CD4 T cell subpopulations in HGSOC omental metastases.

A UMAP showing integrated CD4 T cell clusters from seven patients, 4492 and 5935 cells pre- and post-NACT, respectively. B Heatmap showing top five upregulated genes per cluster. C Differentially expressed genes in NACT versus PDS. Wilcoxon rank sum test. D Violin plot showing the expression of different Treg and exhaustion genes in CD4 clusters. E Slingshot Trajectory analysis for CD4 cell subpopulations. F Circos plot showing TCR repertoire and clonal sharing in CD4 cell clusters coloured by the colour of the cluster. Width of chords reflects clonal sharing. G Percentage CD3 and CD4 T cells in CD45+ cells using flow cytometry on omental samples from HGSOC omenta (n = 8 PDS, n = 23 NACT). Gating on singlet/live/CD45 + /CD3+ cells. Error bars at median and 95%CI. Two-sided Welch t-test. H FOXP3 and TBET positive cells/mm² in 80 HGSOC omenta (PDS = 22, NACT = 58 patients). Error bars at median and 95%CI. Two-sided Mann–Whitney test. I FOXP3 positive cells/mm² comparing PDS and NACT in both BRCA-wild type (n = 42) and BRCAmutated/HRD patients (n = 27). Two-sided Mann–Whitney test. J IHC of human omentum staining for FOXP3 (n = 2 patients) pre- and post-NACT. K i and ii) FOXP3 positive cells/mm² in 42 patient-matched HGSOC samples. iii and iv) Analysis of FOXP3 positive cells/mm² in the patient-matched cohort comparing pre- and post-NACT in both BRCA-wild type (n = 20 paired samples) and BRCAmutated/HRD patients (n = 14 paired samples). Error bars at median and 95%CI. Two-sided Wilcoxon matched-pairs signed rank test. L Kaplan–Meier survival curves (Mantel–Cox) between FOXP3-high and low levels measured by IHC on NACT samples (n = 58). 60% was cut-off between FOXP3 high and low levels. M Expansion index of CD4 TCR in PDS and NACT studied by STARTRAC calculated as 1-normalised Shannon entropy. Error bars at median and 95%CI. Two-sided unpaired student t-test.